Discorded Ponies Series: A series of fics showing the characters being corrupted by Discord from their perspective (including Trixie, who was never corrupted in the series). Nightmare Fuel abounds in all of these, especially the Alternate Ending "Epilogue", which takes place in a horribleBad Future ruled by Discord.

Reharmonized Ponies Series: A sequel series of all original works that follow the canon version of events. Unlike the original, these have a running storyline detailing the ponies' recovery, The Reveal that Trixie is a second Element Of Magic, and Discord's eventual return for round two, once more in a series of POV stories, though some break that formula. While much happier, Nightmare Fuel still abounds.

The Reharmonized Ponies Series itself has some sub-arcs:

Princess Gaia Arc: A continuation of the Reharmonized series, this one completely breaks Fluttershy where Discord couldn't, and in more ways than one.

The "Butterfly" Side Stories: The aftermath of the previous Arc and Applejack breaking the series away from canon, as told from the POV of several Ponies and non-Ponies around Ponyville.

"Origins": A series of stories explaining the origins of Celestia, Discord, Luna, and the end of the G3 World leading to the birth of the G4 one. Gets really dark.

"Mind Games": Things are coming to a head as Diamond Tiara gets closer and closer to freeing Discord. Darkness rises, and chaos might just have the last laugh...

Shining Armor Arc: Shining Armor's backstory and explaining where he's been during the rest of the series.

Wedding Arc: Included due to a poll result. The premise starts the same as the show canon, but things quickly spiral out of control, from the efforts of a muchmore dangerous Queen Chrysalis.

Finale: The Eighth, and apparently final arc of the main series.

There's also the Gaiden: 7 Dreams/Nightmares collection of stories, wherein Princess Luna, Twilight Sparkle, and Pinkie Pie read the journal entries of the seven main G2 ponies, covering the G2 world's change into G3, the Cosmic Retcon of G3, and the collapse of G2 society in the altered timeline through their eyes. Gets pretty dark, but each story tends to lean towards Earn Your Happy Ending territory.

All are rather deep, psychological stories with a Darker and Edgier take on the canon events. Discord is far more sinister and evil, his actions have left deep psychological scars on everypony, and there aren't any quick fixes to the damage inflicted.

What separates this fic from many of the legions of fanfictions out there is just how HUMONGOUS the fic has become. The author regularly tries to create new chapters at a normal rate so that readers aren't Left Hanging, and the fanfiction as written by him is already over 100 chapters long. And not just short chapters. Average word length can be well over 4000 words in places. In addition, the fic has a core of loyal fans who are dedicated not just to creating new original material (as seen below), but for helping contribute to the core material such as the Dreams/Nightmares section mentioned above. Put together, it's quite the story with Continuity, and top notch writing standards from its many editors and creators.

Dark WorldDrabbles: A series of stories taking place in the Dark World timeline that 'reads between the lines' and depicts what the main series didn't, either due to space or because it focused on the mane cast. The first three take place during it (Twilight's actions directly after her Heel-Face Turn, A Day In The Lime Light chapter dealing with the Apple Pie clan, and Discord reconciling with his mortal sister Shady II, but Word of God has stated future chapters will be a Sequel Series taking place after the defeat of Nightmare Eclipse.

Seven Dreams on Nightmare Night: The first part of a mini-arc that may or may not be continued. The spirits of the G2 Mane Seven are allowed to return for one night, and decide to visit their descendants in Ponyville.

Cloudkicker: Rough Day: Cloudkicker has a rough day after Hurricane Fluttershy. Thankfully she has a little sister to return to.

These stories are Loose Canon and it's up to the reader rather or not to consider them canon.

Several Recursive Fanfiction stories have been written in alternate universes as well. As such they are not canon to the main universe, but may be considered elsewhere in the same multiverse. The points of divergence vary, some in ancient past, some closer to modern day. Essentially, these are What If? stories.

Shady: Line Of Fate: Another alternate-universe story by the same author. Warning, big time spoilers for the Origins Arc!

Pinkie Pie's Fourth-Wall Variety Show: A non-canon set of side stories, revolving around the framing device of a fourth-wall breaking "variety show" starring (usually) the mane six, composed of contributions by the main author and fans in a role-playing/collaborative story style.

Part 3, dealing with Magic!Applejack and Twilight being sent to Ponyville for the Summer Sun Celebration and Nightmare Moon's arrival.

Seeds of Knowledge: The story of what Twilight was doing during the Summer Sun Celebration while AJ and the others went after the Elements of Harmony.

Alternate POV Series: Discord World War by KyonSylar: Another official Alternate Universe: (Author Description) "Past and Future are not carved into stone, and each decision can change all the universe. Discord is in war with the world, and this time, he is not alone. The only hope for the world is that the mane six find the second holders of the elements, so that Discord can be stopped once and for all."

Rough Diamonds by Zabuzaacolyte: A shocking and bold alternate course of events for the Reharmonization Series, taking place after Rarity's Reharmonization chapter, Ponyville awakens one morning to find a huge number of foals (including Applebloom and Diamond Tiara), have been kidnapped by the Diamond Dogs. But for what possible purpose? In true Pony POV series fashion, every chapter is another shocking reveal as nothing is as it seems.

Looking Glass Ponies (Part 2, 3, 4, 5, and 6): A look into a world where the wish-granting spell cast at the end of G2 went off without the flaws and an alternate G3 world was made. But can it avoid being erased as well?

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